[2024-01-25 20:06:50,947] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:06:50,949] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:06:50,949] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5df94ad-b4df-414e-90fc-5cdc58f76e2f/dqc_reference
[2024-01-25 20:06:52,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:06:52,099] [INFO] Task started: Prodigal
[2024-01-25 20:06:52,099] [INFO] Running command: gunzip -c /var/lib/cwl/stgc18c820f-4764-4cb6-b32a-4f4357f4d6fd/GCF_003096815.1_ASM309681v1_genomic.fna.gz | prodigal -d GCF_003096815.1_ASM309681v1_genomic.fna/cds.fna -a GCF_003096815.1_ASM309681v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:07,463] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:07,464] [INFO] Task started: HMMsearch
[2024-01-25 20:07:07,464] [INFO] Running command: hmmsearch --tblout GCF_003096815.1_ASM309681v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5df94ad-b4df-414e-90fc-5cdc58f76e2f/dqc_reference/reference_markers.hmm GCF_003096815.1_ASM309681v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:07,663] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:07,664] [INFO] Found 6/6 markers.
[2024-01-25 20:07:07,686] [INFO] Query marker FASTA was written to GCF_003096815.1_ASM309681v1_genomic.fna/markers.fasta
[2024-01-25 20:07:07,686] [INFO] Task started: Blastn
[2024-01-25 20:07:07,686] [INFO] Running command: blastn -query GCF_003096815.1_ASM309681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5df94ad-b4df-414e-90fc-5cdc58f76e2f/dqc_reference/reference_markers.fasta -out GCF_003096815.1_ASM309681v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:08,228] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:08,231] [INFO] Selected 15 target genomes.
[2024-01-25 20:07:08,231] [INFO] Target genome list was writen to GCF_003096815.1_ASM309681v1_genomic.fna/target_genomes.txt
[2024-01-25 20:07:08,244] [INFO] Task started: fastANI
[2024-01-25 20:07:08,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgc18c820f-4764-4cb6-b32a-4f4357f4d6fd/GCF_003096815.1_ASM309681v1_genomic.fna.gz --refList GCF_003096815.1_ASM309681v1_genomic.fna/target_genomes.txt --output GCF_003096815.1_ASM309681v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:16,415] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:16,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5df94ad-b4df-414e-90fc-5cdc58f76e2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:16,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5df94ad-b4df-414e-90fc-5cdc58f76e2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:16,425] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:07:16,425] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:16,425] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Prevotella colorans	strain=DSM 100333	GCA_003096815.1	1703337	1703337	type	True	100.0	945	948	95	conclusive
Prevotella corporis	strain=JCM 8529	GCA_000613365.1	28128	28128	type	True	85.5654	99	948	95	below_threshold
Prevotella corporis	strain=DSM 18810	GCA_000430525.1	28128	28128	type	True	85.439	109	948	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	82.5294	105	948	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	82.4035	101	948	95	below_threshold
Prevotella bergensis	strain=DSM 17361	GCA_000160535.1	242750	242750	type	True	82.0836	239	948	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	79.9961	90	948	95	below_threshold
Prevotella jejuni	strain=DSM 26989	GCA_900187995.1	1177574	1177574	type	True	78.8616	57	948	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	78.0956	155	948	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	77.762	151	948	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	77.6954	151	948	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.9719	80	948	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.9281	100	948	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:16,426] [INFO] DFAST Taxonomy check result was written to GCF_003096815.1_ASM309681v1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:16,427] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:16,427] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:16,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5df94ad-b4df-414e-90fc-5cdc58f76e2f/dqc_reference/checkm_data
[2024-01-25 20:07:16,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:16,458] [INFO] Task started: CheckM
[2024-01-25 20:07:16,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003096815.1_ASM309681v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003096815.1_ASM309681v1_genomic.fna/checkm_input GCF_003096815.1_ASM309681v1_genomic.fna/checkm_result
[2024-01-25 20:08:00,204] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:00,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:00,225] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:00,225] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:00,225] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003096815.1_ASM309681v1_genomic.fna/markers.fasta)
[2024-01-25 20:08:00,226] [INFO] Task started: Blastn
[2024-01-25 20:08:00,226] [INFO] Running command: blastn -query GCF_003096815.1_ASM309681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5df94ad-b4df-414e-90fc-5cdc58f76e2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003096815.1_ASM309681v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:01,001] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:01,004] [INFO] Selected 17 target genomes.
[2024-01-25 20:08:01,004] [INFO] Target genome list was writen to GCF_003096815.1_ASM309681v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:01,021] [INFO] Task started: fastANI
[2024-01-25 20:08:01,022] [INFO] Running command: fastANI --query /var/lib/cwl/stgc18c820f-4764-4cb6-b32a-4f4357f4d6fd/GCF_003096815.1_ASM309681v1_genomic.fna.gz --refList GCF_003096815.1_ASM309681v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003096815.1_ASM309681v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:10,212] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:10,221] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:08:10,222] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003096815.1	s__Prevotella colorans	100.0	945	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000758925.1	s__Prevotella sp000758925	94.3544	719	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430525.1	s__Prevotella corporis	85.4312	109	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.63	97.78	0.92	0.87	4	-
GCF_000426585.1	s__Prevotella baroniae	82.5294	105	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.79	98.01	0.95	0.92	4	-
GCF_000479005.1	s__Prevotella sp000479005	82.3444	123	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.86	96.42	0.92	0.87	3	-
GCF_000160535.1	s__Prevotella bergensis	82.0518	240	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001552765.1	s__Prevotella sp001552765	80.5674	241	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187995.1	s__Prevotella jejuni	78.8177	58	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.57	0.92	0.88	7	-
GCF_000518545.1	s__Prevotella seregens	78.0943	155	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.68	98.64	0.90	0.90	3	-
GCA_900199655.1	s__Prevotella sp900199655	78.0216	94	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.91	99.91	0.98	0.98	2	-
GCA_016901395.1	s__Prevotella sp016901395	77.4811	189	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018789675.1	s__Prevotella sp002300055	76.9281	100	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.15	99.02	0.92	0.90	6	-
GCF_016899955.1	s__Prevotella sp900540415	76.3605	60	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	98.08	0.94	0.91	6	-
GCA_900315835.1	s__Prevotella sp900315835	76.2027	77	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.59	98.19	0.88	0.85	9	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:10,223] [INFO] GTDB search result was written to GCF_003096815.1_ASM309681v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:10,223] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:10,226] [INFO] DFAST_QC result json was written to GCF_003096815.1_ASM309681v1_genomic.fna/dqc_result.json
[2024-01-25 20:08:10,226] [INFO] DFAST_QC completed!
[2024-01-25 20:08:10,226] [INFO] Total running time: 0h1m19s